trinity updated to handle single end reads (they still use se reads)

runTrinitySE.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+# sh runTrinity file1_r1.fq.gz
+# for single end reads just supply one file or multiple files with coma (no space)
+# Runs Trinity, RSEM and calculates alignment stats
+
+READS="--single ${LEFT}"
+CPU=16
+MAXMEM=60G
+
+module load trinityrnaseq/2.1.1
+# Run Trinity with trimming and normalization
+Trinity \
+  --seqType fq \
+  --CPU ${CPU} --max_memory ${MAXMEM} --single "$1" \
+  --normalize_reads \
+  --trimmomatic \
+  --output trinity_out_dir\
+  --no_cleanup
+
+# estimate read abundance (mode RSEM)
+
+${TRINITY_HOME}/util/align_and_estimate_abundance.pl \
+   --transcripts trinity_out_dir/Trinity.fasta \
+   --seqType fq \
+   --single "$1" \
+   --est_method RSEM \
+   --aln_method bowtie2 \
+   --trinity_mode \
+   --prep_reference \
+   --output_dir RSEM_outdir
+
+# estimate read abundance (mode eXpress)
+
+${TRINITY_HOME}/util/align_and_estimate_abundance.pl \
+   --transcripts trinity_out_dir/Trinity.fasta \
+   --seqType fq \
+   --single "$1" \
+   --est_method eXpress \
+   --aln_method bowtie2 \
+   --trinity_mode \
+   --prep_reference \
+   --output_dir eXpress_outdir
+
+
+# run bowtie PE to get alignment stats
+
+${TRINITY_HOME}/util/bowtie_PE_separate_then_join.pl  \
+   --seqType fq \
+   --single "$1" \
+   --target trinity_out_dir/Trinity.fasta \
+   --aligner bowtie2
+
+${TRINITY_HOME}/util/SAM_nameSorted_to_uniq_count_stats.pl \
+   bowtie_out/bowtie_out.nameSorted.bam